MetabolomicsPipeline: An R Package for metabolomics research

An abstract of less than 150 words.

Joel Parker M.S https://publichealth.arizona.edu/departments/epi-bio/biostatistics (University of Arizona) , Bonnie LaFleur PhD https://www.pharmacy.arizona.edu/person/bonnie-lafleur-0 (R. Ken Coit College of PharmacyBio5 Institute)
2024-6-11

1 Introduction

Introduction to Metabolon: * What is Metabolon? * What do they provide their customers (types of analysis).

Limitations of results from metabolon. * Metabolon uses proprietary source code * Additional quality control * Further exploration * Customized analysis * Many plots to sort through * Subpathway hypothesis testing

Introduction to MetabolomomicsPipeline: * Provides users with the tools for an end to end workflow for the analysis of Metabolon data.

Picture of workflow

2 Background

Some packages on interactive graphics include plotly (Sievert 2020) that interfaces with Javascript for web-based interactive graphics, crosstalk (Cheng and Sievert 2021) that specializes cross-linking elements across individual graphics. The recent R Journal paper tsibbletalk (Wang and Cook 2021) provides a good example of including interactive graphics into an article for the journal. It has both a set of linked plots, and also an animated gif example, illustrating linking between time series plots and feature summaries.

3 Customizing tooltip design with ToOoOlTiPs

ToOoOlTiPs is a packages for customizing tooltips in interactive graphics, it features these possibilities.

The palmerpenguins data (Horst et al. 2020) features three penguin species which has a lovely illustration by Alison Horst in Figure 1.

A picture of three different penguins with their species: Chinstrap, Gentoo, and Adelie.

Figure 1: Artwork by @allison_horst

Table 1 prints at the first few rows of the penguins data:

Table 1: A basic table
species island bill_length_mm bill_depth_mm flipper_length_mm body_mass_g sex year
Adelie Torgersen 39.1 18.7 181 3750 male 2007
Adelie Torgersen 39.5 17.4 186 3800 female 2007
Adelie Torgersen 40.3 18.0 195 3250 female 2007
Adelie Torgersen NA NA NA NA NA 2007
Adelie Torgersen 36.7 19.3 193 3450 female 2007
Adelie Torgersen 39.3 20.6 190 3650 male 2007

Figure 2 shows an interactive plot of the penguins data, made using the plotly package.

p <- penguins %>% 
  ggplot(aes(x = bill_depth_mm, y = bill_length_mm, 
             color = species)) + 
  geom_point()
ggplotly(p)

Figure 2: A basic interactive plot made with the plotly package on palmer penguin data. Three species of penguins are plotted with bill depth on the x-axis and bill length on the y-axis. When hovering on a point, a tooltip will show the exact value of the bill depth and length for that point, along with the species name.

5 Summary

We have displayed various tooltips that are available in the package ToOoOlTiPs.

5.1 CRAN packages used

plotly, crosstalk, tsibbletalk, palmerpenguins, ggplot2

5.2 CRAN Task Views implied by cited packages

Phylogenetics, Spatial, TeachingStatistics, TimeSeries, WebTechnologies

J. Cheng and C. Sievert. crosstalk: Inter-widget interactivity for HTML widgets. 2021. URL https://CRAN.R-project.org/package=crosstalk. R package version 1.1.1.
A. M. Horst, A. P. Hill and K. B. Gorman. palmerpenguins: Palmer archipelago (antarctica) penguin data. 2020. URL https://allisonhorst.github.io/palmerpenguins/. R package version 0.1.0.
C. Sievert. Interactive Web-Based Data Visualization with r, plotly, and shiny. Chapman; Hall/CRC, 2020. URL https://plotly-r.com.
E. Wang and D. Cook. Conversations in time: Interactive visualisation to explore structured temporal data. The R Journal, 2021. URL https://journal.r-project.org/archive/2021/RJ-2021-050/index.html.

References

Reuse

Text and figures are licensed under Creative Commons Attribution CC BY 4.0. The figures that have been reused from other sources don't fall under this license and can be recognized by a note in their caption: "Figure from ...".

Citation

For attribution, please cite this work as

M.S & PhD, "MetabolomicsPipeline: An R Package for metabolomics research", The R Journal, 2024

BibTeX citation

@article{main,
  author = {M.S, Joel Parker and PhD, Bonnie LaFleur},
  title = {MetabolomicsPipeline: An R Package for metabolomics research},
  journal = {The R Journal},
  year = {2024},
  issn = {2073-4859},
  pages = {1}
}